Genome-wide identification of novel candidate genes with resistance to biotrophic and necrotrophic pathogens in plants

在所有引起植物疾病的微生物病原体中，一些（称为生物营养菌）靠寄生于活宿主细胞的营养物质而茁壮成长，而另一些（称为坏死营养菌）在定植前或定植过程中杀死宿主细胞，并从死亡宿主组织中吸收营养物质。当抗病性由宿主植物中的主要作用基因控制时，经典的“基因对基因”关系支配着宿主与生物营养病原体的相互作用，而基因对基因的反向关系支配着宿主与坏死性病原体的相互作用。在分子水平上，当植物抗性(R)蛋白识别特定的病原体蛋白（效应器）并引发效应器触发免疫（ETI）时，生物营养性疾病就发生了；坏死性疾病是由非r蛋白介导宿主对坏死性效应物（NEs）[也称为宿主特异性毒素（HSTs）]的识别引起的。然而，小麦和大麦抗病基因的直接分子和功能表征面临的一个巨大挑战是缺乏对其庞大而复杂的基因组的深度和完整测序，因此促使我利用模式植物，拟南芥和短茅中丰富的，未充分利用的基因组资源来推断谷物作物植物的同源抗性基因。本研究将研究谷类植物对一对生物营养性（锈病）和坏死性（褐斑病）病原体的反应，以验证宿主基因组中对生物营养性和坏死性病原体具有部分抗性的基因共享的假设。之所以选择这两种病原体，是因为它们经常同时发生，对加拿大西部和其他地区的谷物生产构成重大威胁。我将开发比较基因组学和生物信息学方法的强大组合，用于全基因组挖掘和发现谷类作物物种中具有抗锈病和褐斑病病原体的候选基因。通过检测和利用拟南芥和谷类之间的高水平种间同源性，将大大提高挖掘能力。提出的全基因组鉴定将揭示两组具有生物营养（锈病）和坏死性（褐斑）病原体抗性的新候选基因的基因组区域模式和分布。我建议对两组基因的基因组位置、结构多样性（例如，调控基因与蛋白质编码基因）、功能多样性（例如，抗性基因在不同基因家族中的分布）以及抗性基因集中在宿主基因组上的可能的“热点”基因组区域进行比较评估，这将阐明围绕对生物营养物和嗜电营养物具有抗性的共享基因的基本问题。该项目的研究结果将对加速加拿大西部谷物锈病和褐斑病同时抗性的遗传改良具有重要意义。

Of all microbial pathogens causing plant diseases, some (known as biotrophs) thrive on nutrients from living host cells while others (known as necrotrophs) kill host cells prior to or during colonization and absorb nutrients from dead host tissues. When disease resistance is controlled by genes of major effects in host plants, the classic `gene-for-gene' relationship governs host interactions with biotrophic pathogens whereas the inverse of gene-for-gene relationship governs host interactions with necrotrophic pathogens. At molecular level, biotrophic diseases occur when plant resistance (R) proteins recognize specific pathogen proteins (effectors) and elicit an effector-triggered immunity (ETI); the necrotrophic diseases arise from the recognition of necrotrophic effectors (NEs) [also known as host-specific toxins (HSTs)] by non-R proteins mediating the host sensitivity to the toxins. However, a huge challenge in direct molecular and functional characterizations of disease-resistance genes in wheat and barley is the lack of deep and complete sequencing of their large and complex genomes, thereby motivating me to exploit the use of rich, underutilized genomic resources available in model plants, Arabidopsis and Brachypodium, for inferring homologous resistance genes in cereal crop plants. This proposal will examine responses to a pair of biotrophic (rusts) and nectrotrophic (tan spot) pathogens in cereal plants to test the hypothesis that there is partial sharing of genes over the host genomes with resistance to both biotrophs and necrotrophs. This pair of pathogens are chosen because they often co-occur and are a major threat to cereal production in western Canada and elsewhere. I will develop a powerful combination of comparative genomics and bioinformatics approaches for genome-wide mining and discovery of candidate genes with resistance to rust and tan spot pathogens in cereal crop species. The mining capability will be greatly enhanced through detecting and utilizing high levels of inter-species homology between Arabidopsis and cereal species. The proposed genome-wide identification will uncover the patterns and distributions of genomic regions at two sets of novel candidate genes with resistance to biotrophic (rusts) and necrotrophic (tan spot) pathogens. My proposed comparative assessment of the two sets of genes in terms of their genomic locations, structural diversity (e.g., regulatory vs. protein-coding genes), functional diversity (e.g., distributions of the resistance genes over different gene families) and possible `hot spot' genomic regions where the resistance genes are concentrated over the host genomes will shed light on the fundamental question surrounding the shared genes with resistance to both biotrophs and nectrotrophs. The results from this proposed project will have important implications for accelerated genetic improvement of simultaneous resistance to cereal rusts and tan spot in western Canada.